Interpretive Summary:
This article represents a linkage map to the switchgrass genome. It was able to clearly distinguish the two subgenomes resulting from whole genome duplication that resulted in the current tetraploid status of the mapping parents. It demonstrates that the two genomes do not readily exchange genetic information. It also clearly shows that the genomes of switchgrass and other grasses are highly collinear. These facts and availability of this map should assist plant breeders in creating better cultivars through more efficient selection.

Technical Abstract:
Switchgrass (Panicum virgatum L.) is being developed as a bioenergy feedstock because it is a high-yielding perennial appropriate for marginal cropland. Switchgrass linkage maps were constructed as a step toward identification of loci underlying quality and yield using simple sequence repeat and sequence tagged markers. Parental maps were created following a two-way pseudo-testcross strategy with segregating single-dose markers in a full-sib family of 238 individuals. These maps coalesced into 18 linkage groups arranged into nine homoeologous pairs. The framework map length and total number of framework and accessory markers were 1376 cM and 563 in the female map and 1645 cM and 541 in the male map. Both framework maps were estimated to place 97 % of the genome within 10 cM of a mapped marker. Near complete preferential pairing was inferred from the ratio of coupling to repulsion phase linkages. Comparative analysis of each homology group to the related sorghum genome identified clear syntenic relationships and collinear tracts. Transmission distorted markers were 3 and 14 % of the single-dose markers in female and male parent, respectively. The male parent is also likely to carry one translocation, detected as the excess of parental genotypic classes between unlinked marker pairs.